WASHINGTON — Neat piles of briefing books and red folders stamped “top secret” blanket the large oak desk that once belonged to General George S. Patton. The national monuments are visible through blast-resistant windows. Steps away, in the custody of a one-star general, are the protocols for ordering the shoot down of a hijacked airliner.

For Ashton B. Carter, his Pentagon office is a far cry from the theoretical jousting of Harvard and MIT’s lecture halls, where he spent much of two decades as one of the nation’s leading national security scholars.

Now he is the Pentagon’s second in command, which makes him the day-to-day manager of the world’s largest bureaucracy at a uniquely challenging time: the military is forced to downsize not in peacetime but as the world grows more unsettled.

That places Carter, 57, in very different circumstances than his predecessors two decades ago, the last time the US military was reduced significantly in size.

“The defense budget was going down and everybody could understand why and accept why — because the Soviet Union had gone away,” the former head of Harvard University’s Belfer Center for Science and International Security, said in an interview. “But we are trying to manage to a lower budget at a time when the threat is not receding.

“The world hasn’t gotten any safer. It’s changing, developing; we’re facing cyber [warfare] and all kinds of new challenges.”

When Carter was elevated to the post of deputy secretary of defense last fall his marching orders from his boss, Secretary of Defense Leon Panetta, highlighted the often competing demands of his broad portfolio.

‘We were paying too much and had become undisciplined.’

Panetta, in designating Carter as his “alter ago,” asked him in a memorandum to give priority to: defeating Al Qaeda and its allies; managing the drawdown of troops in Iraq and Afghanistan; adapting the military to future threats; making sure troops and their families are fully supported; and doing it all with fewer resources.

That, Carter said in an interview with the Globe, often comes down to knowing when — and how — to say no to the military branches, defense agencies, and contractors. But after a decade of nearly unchecked defense spending that’s an answer that has been rarely heard.

On nearly every issue he confronts on a day-to-day basis — on one recent Monday, that included topics as diverse as anti-satellite weapons, nuclear command and control, and veterans’ employment — Carter is confronting powerful constituencies in the military, Congress, and the weapons industry.

Carter said when government and private sector officials seek his support for funding or project approval, he must often ask, sometimes more than once, “What does this have to do with achieving the nation’s defense?”

“That may sound like a simple question,” he explained, “but you have to be disciplined and apply it every day. There is a lot of politics, a lot of bureaucratic inertia.”

He said the Pentagon leadership is trying to be “relentless in our pursuit of better value,” but acknowledged “that is a constant struggle.”

Yet in recent years Carter has gained a reputation for making strides in redirecting the recalcitrant military bureaucracy and taking steps to improve the Pentagon’s buying power.

As the under secretary of defense for acquisition from 2009 to 2011, Carter spurred the reduction or cancellation of dozens of weapons programs deemed ill-suited for modern-day threats or that were mired in cost overruns and development delays.

“After a decade of ever-growing budgets,” Carter said, “we were paying too much and had become undisciplined.”

Earlier this year he shepherded a new defense strategy placing greater emphasis on security in Asia and instituted nearly $500 billion in cuts to projected spending over the next decade.

A sign of Carter’s impact, say some observers, is his reportedly testy relationship with weapons manufacturers.

“Ash Carter is not popular in the defense industry, said Loren Thompson, whose consulting firm, Source Associates, advises a number of contractors. “He is the first guy in a decade who said ‘no’ when the companies wanted something.”

Carter stresses that the defense companies are “our partners” but also makes clear that their agendas are not always in sync.

In one recent speech he bluntly told executives to “look up from the foxhole” and prepare themselves for smaller budgets.

“It’d be great if we had all the money we want,” he told them. “Well, we don’t have all the money we want.”

But on at least one issue Carter and the defense industry are now in lockstep: opposition to more cuts mandated by Congress — on the order of $1.2 trillion, nearly half of which would fall on the Pentagon.

The across-the-board reductions, agreed to last fall as a last-ditch compromise to raise the nation’s debt ceiling, are set to take effect in January unless Congress takes action.

Forcing federal agencies to cut programs equally, as the law stipulates, “takes any strategic discretion out of the process,” Carter said.

“We have adapted to one cut in our budget and we have tried to do that in a strategic way,” he said. “If there is another, we’re going to have to change the strategy.”

Running the Defense Department strikes some as an unlikely role for the brainy former professor. Throughout much of his career Carter was seen as an exceptionally bright policy wonk, not the managerial type.

But many of his current and former colleagues attribute Carter’s success to having experience both in the policy and technical realms – somewhat unusual for national security specialists.

As an undergraduate at Yale University, for example, Carter studied medieval history but he holds a doctorate in theoretical physics, which gives him unique insight into how weapons work.

In 1984 he wrote a paper on missile defense that concluded President Reagan’s prized proposal for a space-based shield — dubbed the “Star Wars” program — was unworkable.

Yet as assistant secretary of defense in the 1990s he was an early champion of the policy to help secure the thousands of nuclear warheads in the former Soviet Union – a program still seen as a model for both non-proliferation efforts and US-Russian cooperation.

“People who try to typecast Ash are always wrong,” said former Secretary of Defense William J. Perry, one of Carter’s mentors.

Carter’s scientific background was especially handy recently when Panetta needed to determine what to do about a particularly nettlesome design problem in the Air Force’s newest fighter jet, the F-22 Raptor, which was depriving pilots of oxygen.

“It is not always clear what the problem is,” Panetta said in a telephone interview. “He was able to understand the intricacies of what is involved.”

“He is one of the bright lights and knows the ins and outs of the Pentagon,” the defense chief added.

Perry said he believes Carter is exactly what the Pentagon needs right now. “He is one of the few government officials who knows the difference between talking and acting.”

Panetta, however, pointed to at least one potential drawback for his intellectual underling: “He cracks jokes that very few people understand.”